Starting phenix.real_space_refine on Thu Sep 18 00:22:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k2x_62000/09_2025/9k2x_62000.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k2x_62000/09_2025/9k2x_62000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k2x_62000/09_2025/9k2x_62000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k2x_62000/09_2025/9k2x_62000.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k2x_62000/09_2025/9k2x_62000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k2x_62000/09_2025/9k2x_62000.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 7850 2.51 5 N 2140 2.21 5 O 2305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12376 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4311 Classifications: {'peptide': 524} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 496} Chain: "B" Number of atoms: 8065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8065 Classifications: {'peptide': 1027} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'CIS': 4, 'PTRANS': 65, 'TRANS': 957} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 6, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 85 Time building chain proxies: 3.30, per 1000 atoms: 0.27 Number of scatterers: 12376 At special positions: 0 Unit cell: (91.135, 156.034, 133.941, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2305 8.00 N 2140 7.00 C 7850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 563.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 15 sheets defined 33.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'A' and resid 601 through 614 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 712 through 724 removed outlier: 3.678A pdb=" N LEU A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Proline residue: A 718 - end of helix Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 772 through 778 Processing helix chain 'A' and resid 782 through 792 Processing helix chain 'A' and resid 818 through 831 Processing helix chain 'A' and resid 833 through 835 No H-bonds generated for 'chain 'A' and resid 833 through 835' Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 917 through 929 Processing helix chain 'A' and resid 958 through 962 Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.873A pdb=" N VAL A 980 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1029 removed outlier: 3.763A pdb=" N VAL A1020 " --> pdb=" O HIS A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1038 Processing helix chain 'A' and resid 1059 through 1063 Processing helix chain 'B' and resid 496 through 519 Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 546 through 553 Processing helix chain 'B' and resid 553 through 568 WARNING: missing atoms! removed outlier: 3.608A pdb=" N ALA B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 577 Processing helix chain 'B' and resid 578 through 588 Processing helix chain 'B' and resid 621 through 632 Processing helix chain 'B' and resid 633 through 636 removed outlier: 4.073A pdb=" N ILE B 636 " --> pdb=" O ALA B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 633 through 636' Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 686 through 690 removed outlier: 3.929A pdb=" N ARG B 690 " --> pdb=" O GLN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 704 Processing helix chain 'B' and resid 801 through 803 No H-bonds generated for 'chain 'B' and resid 801 through 803' Processing helix chain 'B' and resid 805 through 809 Processing helix chain 'B' and resid 826 through 828 No H-bonds generated for 'chain 'B' and resid 826 through 828' Processing helix chain 'B' and resid 842 through 846 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 885 through 889 Processing helix chain 'B' and resid 893 through 907 removed outlier: 3.525A pdb=" N ILE B 907 " --> pdb=" O ARG B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.590A pdb=" N ARG B 974 " --> pdb=" O GLU B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1035 Processing helix chain 'B' and resid 1054 through 1056 No H-bonds generated for 'chain 'B' and resid 1054 through 1056' Processing helix chain 'B' and resid 1071 through 1079 removed outlier: 3.502A pdb=" N TYR B1075 " --> pdb=" O CYS B1071 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY B1079 " --> pdb=" O TYR B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1104 Processing helix chain 'B' and resid 1149 through 1159 Processing helix chain 'B' and resid 1170 through 1181 Processing helix chain 'B' and resid 1190 through 1201 removed outlier: 3.672A pdb=" N LEU B1194 " --> pdb=" O ASP B1190 " (cutoff:3.500A) Processing helix chain 'B' and resid 1236 through 1244 Processing helix chain 'B' and resid 1246 through 1259 removed outlier: 4.043A pdb=" N SER B1250 " --> pdb=" O SER B1246 " (cutoff:3.500A) Processing helix chain 'B' and resid 1270 through 1274 removed outlier: 3.608A pdb=" N PHE B1274 " --> pdb=" O PHE B1271 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1291 Processing helix chain 'B' and resid 1302 through 1305 removed outlier: 3.737A pdb=" N GLY B1305 " --> pdb=" O GLY B1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1302 through 1305' Processing helix chain 'B' and resid 1335 through 1339 Processing helix chain 'B' and resid 1367 through 1372 Processing helix chain 'B' and resid 1394 through 1402 removed outlier: 3.637A pdb=" N GLY B1402 " --> pdb=" O ARG B1398 " (cutoff:3.500A) Processing helix chain 'B' and resid 1418 through 1427 Processing helix chain 'B' and resid 1435 through 1439 Processing helix chain 'B' and resid 1476 through 1480 Processing helix chain 'B' and resid 1498 through 1503 Processing helix chain 'B' and resid 1504 through 1511 removed outlier: 4.017A pdb=" N ASN B1508 " --> pdb=" O ASN B1505 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS B1509 " --> pdb=" O ARG B1506 " (cutoff:3.500A) Processing helix chain 'B' and resid 1549 through 1558 Processing helix chain 'B' and resid 1568 through 1579 removed outlier: 3.566A pdb=" N ALA B1579 " --> pdb=" O GLN B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1581 through 1600 removed outlier: 3.694A pdb=" N GLU B1591 " --> pdb=" O ALA B1587 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B1600 " --> pdb=" O MET B1596 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 592 through 597 removed outlier: 5.294A pdb=" N THR A 659 " --> pdb=" O MET A 625 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 698 through 708 removed outlier: 4.692A pdb=" N LEU A 689 " --> pdb=" O CYS A 702 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS A 704 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 687 " --> pdb=" O HIS A 704 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR A 706 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 685 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ILE A 766 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE A 688 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE A 768 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS A 690 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N LYS A 770 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N TYR A 692 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE A 765 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU A 742 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 814 removed outlier: 4.878A pdb=" N LYS A 874 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N LYS A 875 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 842 " --> pdb=" O LYS A 875 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE A 839 " --> pdb=" O PRO A 852 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYS A 841 " --> pdb=" O GLY A 850 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 905 through 910 removed outlier: 5.063A pdb=" N PHE A 970 " --> pdb=" O LYS A 895 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU A 974 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU A 941 " --> pdb=" O HIS A 953 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 945 " --> pdb=" O ILE A 949 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1002 through 1011 removed outlier: 7.485A pdb=" N ILE A1005 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N HIS A 994 " --> pdb=" O ILE A1005 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 732 through 734 removed outlier: 4.279A pdb=" N VAL B 750 " --> pdb=" O VAL B 734 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 739 through 740 removed outlier: 5.555A pdb=" N LEU B 776 " --> pdb=" O PHE B 797 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS B 793 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU B 782 " --> pdb=" O MET B 791 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET B 791 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU B 819 " --> pdb=" O TRP B 796 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS B 798 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 817 " --> pdb=" O CYS B 798 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 814 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR B 869 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 816 " --> pdb=" O TYR B 869 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 835 " --> pdb=" O TYR B 865 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N LEU B 867 " --> pdb=" O ILE B 835 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 830 through 832 removed outlier: 3.545A pdb=" N SER B 830 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS B 762 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 776 " --> pdb=" O PHE B 797 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS B 793 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU B 782 " --> pdb=" O MET B 791 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET B 791 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU B 819 " --> pdb=" O TRP B 796 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS B 798 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 817 " --> pdb=" O CYS B 798 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 814 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR B 869 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 816 " --> pdb=" O TYR B 869 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 909 through 916 removed outlier: 7.681A pdb=" N ARG B 909 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS B 928 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU B 911 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA B 926 " --> pdb=" O LEU B 911 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLN B 913 " --> pdb=" O TYR B 924 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR B 924 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE B 999 " --> pdb=" O TYR B 923 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N SER B 925 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 12.262A pdb=" N LYS B 997 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 15.444A pdb=" N THR B 927 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 16.944A pdb=" N ARG B 995 " --> pdb=" O THR B 927 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE B 993 " --> pdb=" O PHE B1021 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG B1017 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE B 999 " --> pdb=" O LYS B1015 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS B1015 " --> pdb=" O ILE B 999 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B1020 " --> pdb=" O GLU B1047 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU B1047 " --> pdb=" O LYS B1020 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N TYR B1022 " --> pdb=" O SER B1045 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER B1045 " --> pdb=" O TYR B1022 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 931 through 934 removed outlier: 4.074A pdb=" N ILE B 999 " --> pdb=" O TYR B 923 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N SER B 925 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 12.262A pdb=" N LYS B 997 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 15.444A pdb=" N THR B 927 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 16.944A pdb=" N ARG B 995 " --> pdb=" O THR B 927 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N PHE B1083 " --> pdb=" O ARG B1059 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR B1061 " --> pdb=" O PHE B1083 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE B1085 " --> pdb=" O THR B1061 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B1063 " --> pdb=" O PHE B1085 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AB3, first strand: chain 'B' and resid 1185 through 1187 removed outlier: 8.969A pdb=" N THR B1185 " --> pdb=" O ASP B1162 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B1164 " --> pdb=" O THR B1185 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N PHE B1187 " --> pdb=" O LEU B1164 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA B1166 " --> pdb=" O PHE B1187 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU B1139 " --> pdb=" O ASP B1162 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B1164 " --> pdb=" O LEU B1139 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR B1141 " --> pdb=" O LEU B1164 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA B1166 " --> pdb=" O THR B1141 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP B1143 " --> pdb=" O ALA B1166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1343 through 1344 Processing sheet with id=AB5, first strand: chain 'B' and resid 1385 through 1386 Processing sheet with id=AB6, first strand: chain 'B' and resid 1444 through 1445 removed outlier: 4.043A pdb=" N VAL B1444 " --> pdb=" O ALA B1452 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B1452 " --> pdb=" O VAL B1444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 448 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2658 1.33 - 1.45: 2856 1.45 - 1.57: 7028 1.57 - 1.70: 1 1.70 - 1.82: 123 Bond restraints: 12666 Sorted by residual: bond pdb=" CG GLN A 626 " pdb=" CD GLN A 626 " ideal model delta sigma weight residual 1.516 1.445 0.071 2.50e-02 1.60e+03 8.03e+00 bond pdb=" CB PRO B1260 " pdb=" CG PRO B1260 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.58e+00 bond pdb=" CG PRO B1260 " pdb=" CD PRO B1260 " ideal model delta sigma weight residual 1.503 1.426 0.077 3.40e-02 8.65e+02 5.17e+00 bond pdb=" CA MET A 625 " pdb=" C MET A 625 " ideal model delta sigma weight residual 1.524 1.550 -0.026 1.26e-02 6.30e+03 4.29e+00 bond pdb=" N GLN A 626 " pdb=" CA GLN A 626 " ideal model delta sigma weight residual 1.455 1.478 -0.023 1.23e-02 6.61e+03 3.54e+00 ... (remaining 12661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 16904 3.15 - 6.29: 193 6.29 - 9.44: 25 9.44 - 12.58: 6 12.58 - 15.73: 3 Bond angle restraints: 17131 Sorted by residual: angle pdb=" CA PRO B1260 " pdb=" N PRO B1260 " pdb=" CD PRO B1260 " ideal model delta sigma weight residual 112.00 97.98 14.02 1.40e+00 5.10e-01 1.00e+02 angle pdb=" C GLU B 711 " pdb=" N MET B 712 " pdb=" CA MET B 712 " ideal model delta sigma weight residual 121.70 137.43 -15.73 1.80e+00 3.09e-01 7.63e+01 angle pdb=" CA ARG A 871 " pdb=" CB ARG A 871 " pdb=" CG ARG A 871 " ideal model delta sigma weight residual 114.10 127.08 -12.98 2.00e+00 2.50e-01 4.21e+01 angle pdb=" CA MET A1045 " pdb=" CB MET A1045 " pdb=" CG MET A1045 " ideal model delta sigma weight residual 114.10 124.57 -10.47 2.00e+00 2.50e-01 2.74e+01 angle pdb=" C HIS A 915 " pdb=" N GLY A 916 " pdb=" CA GLY A 916 " ideal model delta sigma weight residual 122.17 117.56 4.61 8.90e-01 1.26e+00 2.68e+01 ... (remaining 17126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6654 17.98 - 35.96: 763 35.96 - 53.94: 210 53.94 - 71.91: 45 71.91 - 89.89: 27 Dihedral angle restraints: 7699 sinusoidal: 3175 harmonic: 4524 Sorted by residual: dihedral pdb=" CA LYS A1033 " pdb=" C LYS A1033 " pdb=" N GLU A1034 " pdb=" CA GLU A1034 " ideal model delta harmonic sigma weight residual 180.00 145.27 34.73 0 5.00e+00 4.00e-02 4.82e+01 dihedral pdb=" CA GLU A1032 " pdb=" C GLU A1032 " pdb=" N LYS A1033 " pdb=" CA LYS A1033 " ideal model delta harmonic sigma weight residual -180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA TYR B1405 " pdb=" C TYR B1405 " pdb=" N GLN B1406 " pdb=" CA GLN B1406 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 7696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1567 0.066 - 0.132: 236 0.132 - 0.198: 21 0.198 - 0.264: 6 0.264 - 0.329: 2 Chirality restraints: 1832 Sorted by residual: chirality pdb=" CB ILE A 797 " pdb=" CA ILE A 797 " pdb=" CG1 ILE A 797 " pdb=" CG2 ILE A 797 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA ARG A 871 " pdb=" N ARG A 871 " pdb=" C ARG A 871 " pdb=" CB ARG A 871 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA LYS A 633 " pdb=" N LYS A 633 " pdb=" C LYS A 633 " pdb=" CB LYS A 633 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1829 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B1259 " 0.110 5.00e-02 4.00e+02 1.54e-01 3.80e+01 pdb=" N PRO B1260 " -0.266 5.00e-02 4.00e+02 pdb=" CA PRO B1260 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO B1260 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 624 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C PRO A 624 " -0.076 2.00e-02 2.50e+03 pdb=" O PRO A 624 " 0.029 2.00e-02 2.50e+03 pdb=" N MET A 625 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1018 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ARG A1018 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG A1018 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU A1019 " -0.019 2.00e-02 2.50e+03 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 348 2.69 - 3.24: 12381 3.24 - 3.80: 19817 3.80 - 4.35: 24880 4.35 - 4.90: 40166 Nonbonded interactions: 97592 Sorted by model distance: nonbonded pdb=" NH2 ARG B1023 " pdb=" O PRO B1361 " model vdw 2.140 3.120 nonbonded pdb=" OG1 THR B 885 " pdb=" OD1 ASN B 888 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR B1494 " pdb=" O ILE B1496 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR B 780 " pdb=" O PHE B 892 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR B 524 " pdb=" OE2 GLU B 547 " model vdw 2.208 3.040 ... (remaining 97587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.890 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 12666 Z= 0.167 Angle : 0.869 15.728 17131 Z= 0.469 Chirality : 0.049 0.329 1832 Planarity : 0.006 0.154 2250 Dihedral : 17.380 89.893 4777 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.45 % Allowed : 23.81 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.21), residues: 1535 helix: -0.08 (0.26), residues: 383 sheet: -0.64 (0.28), residues: 298 loop : -0.16 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 723 TYR 0.015 0.002 TYR A 857 PHE 0.033 0.002 PHE B1274 TRP 0.028 0.002 TRP B1395 HIS 0.008 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00379 (12666) covalent geometry : angle 0.86877 (17131) hydrogen bonds : bond 0.15696 ( 436) hydrogen bonds : angle 6.98713 ( 1161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.517 Fit side-chains TARDY: cannot create tardy model for: "VAL B 561 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 PHE cc_start: 0.8470 (m-80) cc_final: 0.8123 (m-80) REVERT: B 1136 LEU cc_start: 0.9259 (mm) cc_final: 0.8929 (mt) REVERT: B 1260 PRO cc_start: 0.9186 (Cg_exo) cc_final: 0.8701 (Cg_endo) REVERT: B 1544 GLN cc_start: 0.8143 (mt0) cc_final: 0.7899 (mt0) outliers start: 6 outliers final: 4 residues processed: 123 average time/residue: 0.0983 time to fit residues: 18.6570 Evaluate side-chains 114 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 999 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 HIS A 818 ASN A 821 GLN A 855 HIS ** A 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS A1059 ASN B 529 ASN B 790 GLN B 829 HIS B 888 ASN B1026 ASN ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1270 ASN B1332 HIS B1427 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.157045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.102104 restraints weight = 28049.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101168 restraints weight = 15806.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.103772 restraints weight = 11164.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.103361 restraints weight = 8038.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103455 restraints weight = 8660.294| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12666 Z= 0.177 Angle : 0.635 9.361 17131 Z= 0.324 Chirality : 0.044 0.181 1832 Planarity : 0.005 0.069 2250 Dihedral : 4.787 51.776 1702 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 3.06 % Allowed : 21.49 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.21), residues: 1535 helix: 0.47 (0.26), residues: 400 sheet: -0.48 (0.28), residues: 298 loop : -0.02 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1023 TYR 0.012 0.002 TYR A 857 PHE 0.023 0.002 PHE B1274 TRP 0.018 0.001 TRP B1395 HIS 0.003 0.001 HIS A 855 Details of bonding type rmsd covalent geometry : bond 0.00406 (12666) covalent geometry : angle 0.63490 (17131) hydrogen bonds : bond 0.03997 ( 436) hydrogen bonds : angle 5.58827 ( 1161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 GLN cc_start: 0.8163 (mm110) cc_final: 0.7941 (mm110) REVERT: A 637 MET cc_start: 0.6007 (tpp) cc_final: 0.5764 (tpp) REVERT: A 818 ASN cc_start: 0.6833 (OUTLIER) cc_final: 0.6580 (p0) REVERT: B 632 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: B 753 ASP cc_start: 0.8824 (t70) cc_final: 0.8465 (p0) REVERT: B 892 PHE cc_start: 0.7478 (t80) cc_final: 0.7054 (t80) REVERT: B 1136 LEU cc_start: 0.9185 (mm) cc_final: 0.8930 (mt) REVERT: B 1374 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8698 (mm) outliers start: 41 outliers final: 15 residues processed: 152 average time/residue: 0.0915 time to fit residues: 21.8184 Evaluate side-chains 122 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 795 HIS Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1249 VAL Chi-restraints excluded: chain B residue 1274 PHE Chi-restraints excluded: chain B residue 1367 VAL Chi-restraints excluded: chain B residue 1374 LEU Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1421 VAL Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1590 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 63 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 0.2980 chunk 59 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1573 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.156656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101493 restraints weight = 28685.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.100961 restraints weight = 15837.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.103950 restraints weight = 10731.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.103046 restraints weight = 8135.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103630 restraints weight = 8311.703| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12666 Z= 0.167 Angle : 0.605 8.682 17131 Z= 0.307 Chirality : 0.043 0.185 1832 Planarity : 0.005 0.058 2250 Dihedral : 4.441 27.336 1694 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.28 % Allowed : 21.49 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.22), residues: 1535 helix: 0.55 (0.26), residues: 408 sheet: -0.47 (0.28), residues: 307 loop : 0.00 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1023 TYR 0.011 0.001 TYR A 857 PHE 0.023 0.001 PHE B1274 TRP 0.020 0.001 TRP B1395 HIS 0.004 0.001 HIS B1036 Details of bonding type rmsd covalent geometry : bond 0.00384 (12666) covalent geometry : angle 0.60549 (17131) hydrogen bonds : bond 0.03677 ( 436) hydrogen bonds : angle 5.38438 ( 1161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 MET cc_start: 0.6415 (tpp) cc_final: 0.6197 (tpp) REVERT: A 648 MET cc_start: 0.4810 (pmm) cc_final: 0.4514 (pmm) REVERT: B 504 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8298 (mp0) REVERT: B 632 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: B 892 PHE cc_start: 0.7493 (t80) cc_final: 0.6991 (t80) REVERT: B 1136 LEU cc_start: 0.9152 (mm) cc_final: 0.8906 (mt) REVERT: B 1334 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.7328 (t80) outliers start: 44 outliers final: 26 residues processed: 140 average time/residue: 0.0975 time to fit residues: 21.0619 Evaluate side-chains 133 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 795 HIS Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1249 VAL Chi-restraints excluded: chain B residue 1274 PHE Chi-restraints excluded: chain B residue 1334 PHE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1367 VAL Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1421 VAL Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1562 THR Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1596 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 5 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 0.0020 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1573 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.157951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103022 restraints weight = 28266.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.104919 restraints weight = 15158.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.104834 restraints weight = 9255.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.105407 restraints weight = 9445.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.105798 restraints weight = 8160.491| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12666 Z= 0.126 Angle : 0.575 8.597 17131 Z= 0.287 Chirality : 0.042 0.201 1832 Planarity : 0.005 0.070 2250 Dihedral : 4.268 24.247 1694 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.28 % Allowed : 21.34 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1535 helix: 0.75 (0.26), residues: 407 sheet: -0.26 (0.29), residues: 306 loop : 0.07 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1023 TYR 0.012 0.001 TYR B 524 PHE 0.022 0.001 PHE B1274 TRP 0.018 0.001 TRP B1395 HIS 0.004 0.001 HIS B1036 Details of bonding type rmsd covalent geometry : bond 0.00289 (12666) covalent geometry : angle 0.57462 (17131) hydrogen bonds : bond 0.03351 ( 436) hydrogen bonds : angle 5.07429 ( 1161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 611 GLN cc_start: 0.8095 (mm110) cc_final: 0.7842 (mm110) REVERT: A 648 MET cc_start: 0.4607 (pmm) cc_final: 0.4321 (pmm) REVERT: A 737 GLU cc_start: 0.8377 (pp20) cc_final: 0.8160 (pp20) REVERT: A 780 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7641 (mm) REVERT: B 504 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8289 (mp0) REVERT: B 632 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: B 889 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8767 (mmmt) REVERT: B 1136 LEU cc_start: 0.9128 (mm) cc_final: 0.8876 (mt) REVERT: B 1334 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.7321 (t80) REVERT: B 1490 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6946 (ttt180) outliers start: 44 outliers final: 25 residues processed: 150 average time/residue: 0.0957 time to fit residues: 22.2809 Evaluate side-chains 136 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 795 HIS Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1249 VAL Chi-restraints excluded: chain B residue 1274 PHE Chi-restraints excluded: chain B residue 1284 LEU Chi-restraints excluded: chain B residue 1334 PHE Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1374 LEU Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1492 PHE Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1596 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 137 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 108 optimal weight: 8.9990 chunk 48 optimal weight: 50.0000 chunk 25 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 HIS A 728 GLN A 815 ASN A 828 GLN A1012 HIS ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS B1308 GLN B1573 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.152971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.092053 restraints weight = 28553.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094497 restraints weight = 15144.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096180 restraints weight = 10490.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.096969 restraints weight = 8710.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.097565 restraints weight = 7985.099| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12666 Z= 0.232 Angle : 0.647 11.135 17131 Z= 0.325 Chirality : 0.044 0.200 1832 Planarity : 0.005 0.073 2250 Dihedral : 4.481 29.134 1694 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 4.70 % Allowed : 20.37 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1535 helix: 0.62 (0.26), residues: 406 sheet: -0.44 (0.29), residues: 310 loop : -0.04 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1445 TYR 0.017 0.002 TYR B1022 PHE 0.023 0.002 PHE B1274 TRP 0.015 0.002 TRP B1395 HIS 0.008 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00532 (12666) covalent geometry : angle 0.64727 (17131) hydrogen bonds : bond 0.03559 ( 436) hydrogen bonds : angle 5.28534 ( 1161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 106 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 611 GLN cc_start: 0.8068 (mm110) cc_final: 0.7798 (mm110) REVERT: A 801 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7751 (ttpp) REVERT: A 817 MET cc_start: 0.7632 (tpp) cc_final: 0.7431 (tpp) REVERT: B 504 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8241 (mp0) REVERT: B 632 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: B 885 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.7217 (p) REVERT: B 1329 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6934 (mm-30) REVERT: B 1334 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.7284 (t80) outliers start: 63 outliers final: 39 residues processed: 158 average time/residue: 0.0993 time to fit residues: 24.0686 Evaluate side-chains 143 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain B residue 529 ASN Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 795 HIS Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1038 ASP Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1165 TRP Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1249 VAL Chi-restraints excluded: chain B residue 1256 ASP Chi-restraints excluded: chain B residue 1274 PHE Chi-restraints excluded: chain B residue 1279 VAL Chi-restraints excluded: chain B residue 1284 LEU Chi-restraints excluded: chain B residue 1329 GLU Chi-restraints excluded: chain B residue 1334 PHE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1367 VAL Chi-restraints excluded: chain B residue 1374 LEU Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1492 PHE Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1536 GLN Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1562 THR Chi-restraints excluded: chain B residue 1580 VAL Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1596 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 5 optimal weight: 0.0970 chunk 9 optimal weight: 7.9990 chunk 153 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 chunk 8 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS A1025 GLN B 529 ASN B 555 GLN ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1573 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.154470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.093433 restraints weight = 27992.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096269 restraints weight = 14450.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098000 restraints weight = 9999.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099044 restraints weight = 8293.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.099282 restraints weight = 7549.372| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12666 Z= 0.149 Angle : 0.602 10.671 17131 Z= 0.299 Chirality : 0.043 0.349 1832 Planarity : 0.005 0.061 2250 Dihedral : 4.344 26.786 1694 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.73 % Allowed : 20.90 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.22), residues: 1535 helix: 0.87 (0.26), residues: 405 sheet: -0.48 (0.29), residues: 316 loop : 0.09 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1023 TYR 0.012 0.001 TYR B1563 PHE 0.023 0.001 PHE B1274 TRP 0.015 0.001 TRP B1395 HIS 0.009 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00348 (12666) covalent geometry : angle 0.60214 (17131) hydrogen bonds : bond 0.03340 ( 436) hydrogen bonds : angle 5.10336 ( 1161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 105 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8542 (pmm) cc_final: 0.7883 (pmm) REVERT: A 611 GLN cc_start: 0.8042 (mm110) cc_final: 0.7770 (mm110) REVERT: B 504 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8234 (mp0) REVERT: B 632 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8334 (m-80) REVERT: B 892 PHE cc_start: 0.7460 (t80) cc_final: 0.7054 (t80) REVERT: B 1329 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6850 (mm-30) REVERT: B 1334 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.7301 (t80) REVERT: B 1439 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7468 (tt) REVERT: B 1451 MET cc_start: 0.7054 (tmm) cc_final: 0.6424 (tmm) outliers start: 50 outliers final: 34 residues processed: 146 average time/residue: 0.0965 time to fit residues: 21.9941 Evaluate side-chains 136 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 795 HIS Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 999 ILE Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1165 TRP Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1249 VAL Chi-restraints excluded: chain B residue 1256 ASP Chi-restraints excluded: chain B residue 1274 PHE Chi-restraints excluded: chain B residue 1284 LEU Chi-restraints excluded: chain B residue 1329 GLU Chi-restraints excluded: chain B residue 1334 PHE Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1374 LEU Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1492 PHE Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1536 GLN Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1562 THR Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1596 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 58 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 104 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 141 optimal weight: 0.0670 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS A1025 GLN B 529 ASN ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1573 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.155054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094299 restraints weight = 27887.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.096398 restraints weight = 14873.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.098359 restraints weight = 10255.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099242 restraints weight = 8405.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.099771 restraints weight = 7673.770| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12666 Z= 0.135 Angle : 0.600 9.855 17131 Z= 0.296 Chirality : 0.043 0.308 1832 Planarity : 0.005 0.068 2250 Dihedral : 4.280 24.738 1694 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.18 % Allowed : 20.97 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.22), residues: 1535 helix: 0.98 (0.27), residues: 400 sheet: -0.43 (0.29), residues: 316 loop : 0.12 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1490 TYR 0.011 0.001 TYR B1240 PHE 0.022 0.001 PHE B1274 TRP 0.011 0.001 TRP B1395 HIS 0.008 0.001 HIS A1012 Details of bonding type rmsd covalent geometry : bond 0.00314 (12666) covalent geometry : angle 0.60022 (17131) hydrogen bonds : bond 0.03205 ( 436) hydrogen bonds : angle 5.00461 ( 1161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 106 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 GLN cc_start: 0.8002 (mm110) cc_final: 0.7749 (mm110) REVERT: A 637 MET cc_start: 0.6219 (mmt) cc_final: 0.5823 (mmt) REVERT: A 787 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8470 (t80) REVERT: B 504 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8231 (mp0) REVERT: B 632 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: B 1235 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: B 1329 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: B 1334 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.7287 (t80) REVERT: B 1439 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7483 (tt) outliers start: 56 outliers final: 40 residues processed: 155 average time/residue: 0.0956 time to fit residues: 23.3552 Evaluate side-chains 150 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 795 HIS Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 985 LEU Chi-restraints excluded: chain B residue 999 ILE Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1249 VAL Chi-restraints excluded: chain B residue 1256 ASP Chi-restraints excluded: chain B residue 1274 PHE Chi-restraints excluded: chain B residue 1284 LEU Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1329 GLU Chi-restraints excluded: chain B residue 1334 PHE Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1374 LEU Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1492 PHE Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1536 GLN Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1562 THR Chi-restraints excluded: chain B residue 1580 VAL Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1596 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 45 optimal weight: 40.0000 chunk 98 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1181 ASN B1573 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.151107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.095628 restraints weight = 27968.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097144 restraints weight = 15578.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.098499 restraints weight = 10361.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098001 restraints weight = 9425.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097969 restraints weight = 8880.114| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12666 Z= 0.268 Angle : 0.689 12.187 17131 Z= 0.346 Chirality : 0.045 0.222 1832 Planarity : 0.005 0.064 2250 Dihedral : 4.644 31.479 1694 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 4.10 % Allowed : 21.04 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.22), residues: 1535 helix: 0.76 (0.26), residues: 399 sheet: -0.58 (0.29), residues: 315 loop : -0.17 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1555 TYR 0.020 0.002 TYR B1022 PHE 0.024 0.002 PHE B1274 TRP 0.014 0.002 TRP B1498 HIS 0.024 0.002 HIS A1012 Details of bonding type rmsd covalent geometry : bond 0.00611 (12666) covalent geometry : angle 0.68883 (17131) hydrogen bonds : bond 0.03584 ( 436) hydrogen bonds : angle 5.31596 ( 1161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 103 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.9079 (pmm) cc_final: 0.8403 (pmm) REVERT: A 625 MET cc_start: 0.8346 (tpp) cc_final: 0.8126 (tpp) REVERT: A 787 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8794 (t80) REVERT: B 504 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8269 (mp0) REVERT: B 632 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: B 718 MET cc_start: 0.4802 (tpt) cc_final: 0.4522 (tpt) REVERT: B 1082 ARG cc_start: 0.8700 (mtt180) cc_final: 0.7949 (mtt180) REVERT: B 1235 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: B 1329 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6872 (mm-30) REVERT: B 1334 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.7291 (t80) REVERT: B 1439 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7555 (tt) REVERT: B 1451 MET cc_start: 0.7316 (tmm) cc_final: 0.6777 (tmm) REVERT: B 1527 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8445 (m) outliers start: 55 outliers final: 45 residues processed: 149 average time/residue: 0.0908 time to fit residues: 21.2967 Evaluate side-chains 152 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 100 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 795 HIS Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 985 LEU Chi-restraints excluded: chain B residue 999 ILE Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1038 ASP Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1165 TRP Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1249 VAL Chi-restraints excluded: chain B residue 1256 ASP Chi-restraints excluded: chain B residue 1274 PHE Chi-restraints excluded: chain B residue 1284 LEU Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1329 GLU Chi-restraints excluded: chain B residue 1334 PHE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1365 ILE Chi-restraints excluded: chain B residue 1367 VAL Chi-restraints excluded: chain B residue 1374 LEU Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1420 LEU Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1492 PHE Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1536 GLN Chi-restraints excluded: chain B residue 1562 THR Chi-restraints excluded: chain B residue 1580 VAL Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1596 MET Chi-restraints excluded: chain B residue 1597 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 12 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 56 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1573 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.151931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.095182 restraints weight = 28175.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098026 restraints weight = 16004.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097929 restraints weight = 10698.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098418 restraints weight = 9843.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.098468 restraints weight = 8899.009| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12666 Z= 0.205 Angle : 0.666 11.459 17131 Z= 0.327 Chirality : 0.044 0.212 1832 Planarity : 0.005 0.064 2250 Dihedral : 4.594 29.426 1694 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.81 % Allowed : 21.57 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.22), residues: 1535 helix: 0.77 (0.26), residues: 400 sheet: -0.56 (0.29), residues: 312 loop : -0.15 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1490 TYR 0.016 0.002 TYR B1022 PHE 0.024 0.002 PHE B1274 TRP 0.014 0.002 TRP B1498 HIS 0.005 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00471 (12666) covalent geometry : angle 0.66556 (17131) hydrogen bonds : bond 0.03401 ( 436) hydrogen bonds : angle 5.21343 ( 1161) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.9018 (pmm) cc_final: 0.8439 (pmm) REVERT: A 787 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8744 (t80) REVERT: A 813 LEU cc_start: 0.6686 (mm) cc_final: 0.5866 (mm) REVERT: B 504 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8294 (mp0) REVERT: B 555 GLN cc_start: 0.7177 (pp30) cc_final: 0.6969 (tm-30) REVERT: B 587 LEU cc_start: 0.7544 (mt) cc_final: 0.7113 (pp) REVERT: B 632 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: B 1235 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8128 (m-80) REVERT: B 1329 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6900 (mm-30) REVERT: B 1334 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.7302 (t80) REVERT: B 1439 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7530 (tt) REVERT: B 1451 MET cc_start: 0.7090 (tmm) cc_final: 0.6538 (tmm) outliers start: 51 outliers final: 38 residues processed: 146 average time/residue: 0.0898 time to fit residues: 20.7483 Evaluate side-chains 143 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 795 HIS Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 999 ILE Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1165 TRP Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1249 VAL Chi-restraints excluded: chain B residue 1256 ASP Chi-restraints excluded: chain B residue 1274 PHE Chi-restraints excluded: chain B residue 1284 LEU Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1329 GLU Chi-restraints excluded: chain B residue 1334 PHE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1365 ILE Chi-restraints excluded: chain B residue 1367 VAL Chi-restraints excluded: chain B residue 1374 LEU Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1562 THR Chi-restraints excluded: chain B residue 1580 VAL Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1596 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 0.0770 chunk 14 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 132 optimal weight: 0.0270 chunk 129 optimal weight: 0.0770 chunk 56 optimal weight: 0.0980 chunk 33 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B1036 HIS ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1308 GLN B1573 HIS ** B1575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.156405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.097688 restraints weight = 28094.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099373 restraints weight = 14462.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.100755 restraints weight = 9757.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102259 restraints weight = 8056.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.102579 restraints weight = 7173.150| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12666 Z= 0.107 Angle : 0.631 13.587 17131 Z= 0.305 Chirality : 0.043 0.256 1832 Planarity : 0.004 0.064 2250 Dihedral : 4.278 25.308 1694 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.61 % Allowed : 23.28 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.22), residues: 1535 helix: 0.96 (0.27), residues: 408 sheet: -0.31 (0.30), residues: 306 loop : 0.13 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1023 TYR 0.013 0.001 TYR A 857 PHE 0.019 0.001 PHE B1274 TRP 0.013 0.001 TRP B1498 HIS 0.010 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00238 (12666) covalent geometry : angle 0.63062 (17131) hydrogen bonds : bond 0.03015 ( 436) hydrogen bonds : angle 4.83240 ( 1161) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8639 (pmm) cc_final: 0.8040 (pmm) REVERT: A 787 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8582 (t80) REVERT: A 813 LEU cc_start: 0.6581 (mm) cc_final: 0.5954 (mm) REVERT: B 504 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8246 (mp0) REVERT: B 555 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: B 632 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: B 753 ASP cc_start: 0.8687 (t0) cc_final: 0.8303 (p0) REVERT: B 892 PHE cc_start: 0.7401 (t80) cc_final: 0.7085 (t80) REVERT: B 1082 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8212 (mtt180) REVERT: B 1235 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8181 (m-80) REVERT: B 1264 LEU cc_start: 0.8622 (tp) cc_final: 0.8268 (tp) REVERT: B 1284 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8206 (mm) REVERT: B 1314 ILE cc_start: 0.8100 (mm) cc_final: 0.7886 (mt) REVERT: B 1329 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: B 1334 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7314 (t80) REVERT: B 1435 ASP cc_start: 0.7826 (p0) cc_final: 0.7379 (p0) REVERT: B 1439 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7405 (tt) REVERT: B 1451 MET cc_start: 0.6884 (tmm) cc_final: 0.6260 (tmm) REVERT: B 1544 GLN cc_start: 0.8013 (mt0) cc_final: 0.7700 (mt0) outliers start: 35 outliers final: 26 residues processed: 136 average time/residue: 0.0960 time to fit residues: 20.4205 Evaluate side-chains 138 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 795 HIS Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 999 ILE Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1249 VAL Chi-restraints excluded: chain B residue 1256 ASP Chi-restraints excluded: chain B residue 1274 PHE Chi-restraints excluded: chain B residue 1284 LEU Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1329 GLU Chi-restraints excluded: chain B residue 1334 PHE Chi-restraints excluded: chain B residue 1357 LEU Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1573 HIS Chi-restraints excluded: chain B residue 1580 VAL Chi-restraints excluded: chain B residue 1594 LEU Chi-restraints excluded: chain B residue 1596 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 62 optimal weight: 30.0000 chunk 95 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 134 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.155671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095325 restraints weight = 28139.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.097696 restraints weight = 15037.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099477 restraints weight = 10493.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.100106 restraints weight = 8670.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.100766 restraints weight = 8025.655| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12666 Z= 0.112 Angle : 0.636 16.438 17131 Z= 0.305 Chirality : 0.043 0.235 1832 Planarity : 0.004 0.063 2250 Dihedral : 4.206 24.805 1694 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.54 % Allowed : 23.28 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.22), residues: 1535 helix: 1.00 (0.27), residues: 408 sheet: -0.20 (0.30), residues: 300 loop : 0.14 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1490 TYR 0.015 0.001 TYR B1084 PHE 0.019 0.001 PHE B1274 TRP 0.010 0.001 TRP B1498 HIS 0.009 0.001 HIS B1036 Details of bonding type rmsd covalent geometry : bond 0.00259 (12666) covalent geometry : angle 0.63636 (17131) hydrogen bonds : bond 0.03003 ( 436) hydrogen bonds : angle 4.78469 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3260.10 seconds wall clock time: 56 minutes 42.76 seconds (3402.76 seconds total)